Legionellosis as an emergent disease

DEEP-SUBSURFACE MICROBIAL COMMUNITIES: DIVERSITY AND ACTIVITY

Introduction

If we can remark something of the main characteristics of our planet, is the huge diversity of organisms. From the largest and most complex mammals to smaller and simpler organisms. All of them play an essential role in the ecosystem and its regulation. The big organisms could not live without the smaller organisms and in such a way it happens the reverse. Therefore, exists a dependence between each other. In this blog we will talk about the second group of organisms, "The smallest, most essential and large colonizers of adverse environments: the microorganisms of the depths of the subsurface. With such a surprising diversity of organisms in such an extreme environment, the deep subsurface has been the subject of many studies in the recent years. Deep subsurface microbes carry out processes that alter the chemical make up of minerals, degrade pollutants, and alter the mineral content of ground water. Many of them can also break down petroleum substances, which has been utilized in cleaning up oil spills and other accidents of that nature. Studies are being done to search for deep subsurface microbes that produce antibiotics and heat stable enzymes, and for those that assist in the degradation of toxic substances. Due to the massive amount of habitable area, and the surprisingly high density in which these microbes live, it is now believed that subsurface microbes are responsible for over half of the biomass on the planet.

Microbial communities on the deep-subsurface

Deep-subsurface

The study of these communities of microorganisms is carried out by taking advantage of deep mines.

The communities of microorganisms that are found on the deep-subsurface of the aquatic environment, live in ranges of depth that oscillate between 50 meters below the terrestrial surface and are stretched up to 3 km (Figure 1). The organisms live within theflooded pore space within the rocks and live by reducing inorganic compounds found in the rock (some of them degrade rocks by enzymes to obtain nutrients and energy to maintain a minimum metabolic activity). The depth of these habitats determines the temperature at which the microorganisms are found; there is a direct relationship between both variables, the deeper, the more temperature. The gradient of the earth's crust is 25º/km (according to contrasted sources). The maximum temperature at which these microorganisms can be found is 110º. 
The temperature also determines the density of the populations of these microorganisms, there is a gradual decrease of the density of the cells with the increase of the temperature, likewise, it is possible to find individual isolated cells as well as 100 million individuals per gram of rock. These densities are also limited by the availability of space in the substrate.
The different types of habitat are: hydrothermal waters, metamorphic rocks and crystalline ignitions and sedimentary basins/oil reservoirs.
The microbial communities are formed by bacterial and archaeal species which are specialized in inorganic substrate oxidation, with iron and sulfur oxidation, the two main energy sources. The three main key organisms are: thermophiles, heterotrophs and lithorophs. 

                                         

Figure 1: Local, intermediate and regional flow systems in the lithosphere. Deep subsurface refers to area where intermediate or regional flows occur.

Thermophiles

Thermophiles are microbes that have adapted to living in extremely hot environments. These environments occur deep in the rocks near the magma layer, or within the hydrothermal waters deep under the ocean floor. (https://microbewiki.kenyon.edu/index.php/Deep_subsurface_microbes).

Diverse bacteria and archaea require the temperatures found in geothermal environments for optimal growth, and are classified as extreme thermophiles. Extreme thermophiles use two basic strategies to avoid thermal denaturation of their enzymes: extrinsic stabilisation, conferred by certain small molecules, and intrinsic stabilisation, conferred by the specific structure and conformation of the enzyme itself.

Ex: Bacillus stearothermophilus

Heterotrophs

The heterotrophs metabolism is used by organisms requiring organic compounds for growth and reproduction; the organic compounds serve as sources of carbon and energy (Atlas i Bartha, 1998).

Energy is still usually derived from the reduced inorganic substrates, but some derive both energy and carbon from hydrocarbons.

Ex:  Oscillatoria limnetica

Lithotrophs

Lithotrophs obtain energy from the oxidation of soluble inorganic compounds. These organisms are considered primary producers and constitute the largest portion of biomass in the deep subsurface biosphere. (https://microbewiki.kenyon.edu/index.php/Deep_subsurface_microbes).

Lithotrophs use reduced sulfur compounds. Is the most common strategy here, and is carried out by the largest number of microorganisms. Most lithotrophs use the CO₂ that is trapped in the rocks as their source of carbon.

Ex:  Desulfovibrio profundus

Adaptation and metabolism

All of this types of microorganisms have different kinds of adaptations like: cope with the nutrient limitations, dessication resistance, radiation resistance and DNA repair mechanisms.

Below we find the different metabolisms that take place in the deep-subsurface.

Anaerobic respiration

Due to the lack of oxygen in the deep subsurface many microbes were forced to rely on other types of compounds as electron acceptors to be able to adapt and survive. These types of microbes are anaerobic respirators, it consists in a biological process where the electron acceptor is different from oxygen, it is usually nitrate or sulphate. This type of respiration should not be confused with fermentation because an electron transport chain does not participate and the final acceptor of electrons is always an organic molecule such as pyruhere are different types of anaerobic respiration.

Lithotrophy

Lithotrophs are a diverse group of organisms that use inorganic substrates (iron, sulfur and magnesium) in order to achieve reducers for use in biosynthesis or energy conservation through anaerobic respiration. they eliminate electrons from a substrate and transmit them through an electron transport system that will produce ATP by phosphorylation of the transport of electrons. Hydrogen is the main electron donor, although other compounds are also used:

Methanogenesis

The methanogenesis is the process of formation of methane that living beings do, normally it is the final step of the decomposition of the biomass.

There are two types of methanogenesis:

Production of methane by reduction of CO₂: It’s a form of anaerobic respiration. The final electron acceptor is carbon (Figure 2).

Figure 2: Production of methane by reduction of CO_2.

Methane production from organic molecules: Produce methane from simple organic substrates (acetic acid, methanol).

Hydrocarbon degredation

Heterotrophic microorganisms that live in anaerobic conditions with abundant hydrocarbons metabolize these hydrocarbons as a source of energy and carbon (Figure 3).

These types of microorganisms are used for the degradation and cleaning of disasters related to oil and its distilled forms.

Figure 3: Hydrocarboon degredation

Due to the different environments and characteristics of the communities of microorganisms, they have to look for different sources of energy and exploit several metabolic pathways, including nitrate, sulfate, manganese and iron reduction, sulphur oxidation, methanogenesis, acetogenesis and anaerobic methane oxidation (AOM) (Table 1).

Table 1:  Microbial's metabolism

MICROBIAL PROCESS	ELECTRON DONOR	ELECTRON ACCEPTOR
Acetogenesis	H2	CO2
Anaerobic methane oxidation	CH4	SO42-
Denitrification	H2	NO3-
Methanogenesis	H2	CO2
Sulfate reduction	H2	SO42-
Sulfur reduction	H2	S0

Conclusions

The ability of these microorganisms to live in anaerobic environments and completely hostile and extreme conditions, has focused and enhanced research on the use of these organisms as possible solutions or alternatives to impacts or problems in the environment. Degrading oil, feeding on plastics in the ocean, assimilation through its metabolism of compounds are harmful to the environment, ... The extraordinary activity of these organisms could mean the end of many bad environmental problems and problems of our society.

We often forget the potential of these microorganisms and their importance in our lives. We should be aware that without these small organisms, we would not be here.

Bibliography 

Andreas eTeske, Jennifer F Biddle, Virginia P Edgcomb, & Axel eSchippers. (2013). Deep Subsurface Microbiology: A guide to the Research topic papers. Frontiers in Microbiology, Vol 4 (2013). 

McKelvie, J. R., Korber, D. R., & Wolfaardt, G. M. (2016). Microbiology of the Deep Subsurface Geosphere and Its Implications for Used Nuclear Fuel Repositories. Their World: A Diversity of Microbial Environments, 251

Bartha, R. (1986). Applying Microbiology. BioScience, 36(5), 344.  

Escudero, C., Oggerin, M., & Amils, R. (n.d.). The deep continental subsurface: the dark biosphere.

- Widdle, F. Rabus, R. Anaerobic biodegradation of saturated ad aromatic hidrocarbons. Recuperat de 
http://bioinformatica.uab.es/biocomputacio/treballs0203/RBurgos/dades/Articulos/Anarerobicdegradation.pdf

-- https://microbewiki.kenyon.edu/index.php/Deep_subsurface_microbes

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Here are some news web links about microorganisms that live in the subsoil and have a relationship or impact on the environment or are the trainers of some material.

- https://noticiasdelaciencia.com/art/3319/bacterias-capaces-de-vivir-en-el-subsuelo-de-marte 

- Anònim, Descubren bacterias alienígenas que viven sin oxígeno en el subsuelo de Sevilla como si tal cosa. Recuperat de: https://www.periodistadigital.com/ciencia/medioambiente/2014/08/29/descubren-a-unas escurridizas-bacterias-alienigenas-en-las-profundidades-de-sevilla.shtml 

- Álvarez, C., Unas bacterias eliminan el cloro como nosotros nos comemos una hamburguesa. Recuperat de: https://elpais.com/diario/2006/10/04/futuro/1159912802_850215.html 

These types of microorganisms are used for the degradation and cleaning of disasters related to oil and its distilled forms.

These types of microorganisms are used for the degradation and cleaning of disasters related to oil and its distilled forms.